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- PDB-5jso: Structures of DddQ from Ruegeria lac. Reveal Key Residues for Met... -

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Basic information

Entry
Database: PDB / ID: 5jso
TitleStructures of DddQ from Ruegeria lac. Reveal Key Residues for Metal Binding and Catalysis - TRIS bound
ComponentsDimethlysulfonioproprionate lyase DddQ
KeywordsLYASE / dimethylsulfoniopropionate / cupin / metalloenzyme
Function / homology
Function and homology information


dimethylpropiothetin dethiomethylase / dimethylpropiothetin dethiomethylase activity / metal ion binding
Similarity search - Function
Dimethlysulfonioproprionate lyase / Dimethlysulfonioproprionate lyase / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Dimethylsulfoniopropionate lyase DddQ
Similarity search - Component
Biological speciesRuegeria lacuscaerulensis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBrummett, A.E. / Dey, M.
Funding support United States, 1items
OrganizationGrant numberCountry
University of Iowa, College of Liberal Arts and Sciences United States
CitationJournal: Biochemistry / Year: 2016
Title: New Mechanistic Insight from Substrate- and Product-Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase DddQ.
Authors: Brummett, A.E. / Dey, M.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dimethlysulfonioproprionate lyase DddQ
B: Dimethlysulfonioproprionate lyase DddQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,41512
Polymers44,7902
Non-polymers62510
Water6,287349
1
A: Dimethlysulfonioproprionate lyase DddQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6445
Polymers22,3951
Non-polymers2494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dimethlysulfonioproprionate lyase DddQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7717
Polymers22,3951
Non-polymers3766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.870, 87.761, 48.900
Angle α, β, γ (deg.)90.000, 93.370, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dimethlysulfonioproprionate lyase DddQ / DMSP lyase


Mass: 22395.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria lacuscaerulensis (strain DSM 11314 / KCTC 2953 / ITI-1157) (bacteria)
Strain: DSM 11314 / KCTC 2953 / ITI-1157 / Gene: dddQ, SL1157_0332 / Production host: Escherichia coli (E. coli)
References: UniProt: D0CY60, dimethylpropiothetin dethiomethylase

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Non-polymers , 5 types, 359 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.0, 0.2 M LiCl, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97625 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Aug 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→48.817 Å / Num. all: 26468 / Num. obs: 26468 / % possible obs: 99 % / Redundancy: 3.7 % / Biso Wilson estimate: 14.98 Å2 / Rpim(I) all: 0.046 / Rrim(I) all: 0.088 / Rsym value: 0.063 / Net I/av σ(I): 10.467 / Net I/σ(I): 14.1 / Num. measured all: 97454
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.113.60.223.51404738530.1610.310.225.199
2.11-2.243.70.1584.91341436650.1150.2220.1586.999.5
2.24-2.393.70.1236.31249234010.0890.1710.1238.998.7
2.39-2.583.80.0898.41214232330.0650.1260.0891199.7
2.58-2.833.70.07210.31079229130.0520.10.0721499
2.83-3.163.70.05512.9992026720.0390.0760.05518.299.1
3.16-3.653.70.04216860123510.030.0580.04222.898.3
3.65-4.473.60.03517.6711819600.0250.0480.03527.397.8
4.47-6.323.70.03216.6577115560.0230.0440.03227.299.4
6.32-48.8173.70.0291931578640.0220.0410.02928.397.9

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.2data extraction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LA2

4la2


Resolution: 2→48.816 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2362 1239 4.68 %4.7%
Rwork0.1854 25210 --
obs0.1878 26449 98.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 48.43 Å2 / Biso mean: 15.904 Å2 / Biso min: 1.81 Å2
Refinement stepCycle: final / Resolution: 2→48.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 29 349 3319
Biso mean--26.67 23.89 -
Num. residues----380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133084
X-RAY DIFFRACTIONf_angle_d0.8194218
X-RAY DIFFRACTIONf_chiral_restr0.05439
X-RAY DIFFRACTIONf_plane_restr0.006545
X-RAY DIFFRACTIONf_dihedral_angle_d16.7591057
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.08010.25861560.20052747290399
2.0801-2.17480.27861330.19272810294399
2.1748-2.28940.27281150.20092802291798
2.2894-2.43280.28111050.188428712976100
2.4328-2.62070.2551280.193828142942100
2.6207-2.88440.24791730.19222770294399
2.8844-3.30170.2371270.1872818294599
3.3017-4.15940.19651280.16932784291298
4.1594-48.83010.21071740.17672794296898

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